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Open Access Research article

Selective Phenotyping, Entropy Reduction, and the Mastermind game

Julien Gagneur1*, Markus C Elze2 and Achim Tresch3

Author Affiliations

1 European Molecular Biology Lab, 69122 Heidelberg, Germany

2 Johannes Gutenberg-University, 55099 Mainz, Germany

3 Gene Center, Ludwig-Maximilians-University, 81377 Munich, Germany

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BMC Bioinformatics 2011, 12:406  doi:10.1186/1471-2105-12-406

Published: 20 October 2011

Abstract

Background

With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately.

Results

Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of previously phenotyped individuals, thereby enabling an efficient incremental strategy. The effective performance of SPARE is demonstrated on simulated data as well as on an experimental yeast dataset.

Conclusions

Using entropy reduction as an objective criterion gives a natural way to tackle both issues of detection and localization simultaneously and to integrate intermediate phenotypic data. We foresee entropy-based strategies as a fruitful research direction for selective phenotyping.